Discovery and Targeted Proteomics, HRMS Characterization by PhDs at 20+ Year, FDA-Inspected Lab

At every stage where a molecule must be identified or measured. Discovery chemistry leans on it to confirm and rank compounds; preclinical development runs dose range finding and GLP toxicokinetics on LC-MS/MS in rodent and non-rodent species; clinical programs quantify drug and metabolites through submission. High-resolution instruments add the identification layer: metabolite ID, proteomics and characterization questions that quantitation-only platforms cannot answer.

Mass spec proteomics service is a mass spectrometry analysis service that studies proteins and peptides in biological samples. Scientists use mass spec proteomics services to identify proteins, quantify their expression, characterize their modifications, and investigate their interactions and functions. Mass spec proteomics services can provide valuable information for drug development or discovery, disease diagnosis, and biomedical research.

HRMS stands for high-resolution mass spectrometry, a type of mass spectrometry that can measure the mass of ions with very high accuracy and precision, usually in the range of parts per million (ppm) or less. Scientists can use HRMS to determine the exact molecular formula and structure of unknown compounds and distinguish between isomers and isotopes. HRMS can also perform qualitative and quantitative analysis of complex mixtures, such as proteomics and metabolomics samples.

The working set here is compact. Electrospray ionization brings molecules into the gas phase from LC flow; LC-MS/MS on triple quadrupoles carries validated quantitation; and high-resolution accurate mass on the Q Exactive HF Orbitrap carries identification: DDA and DIA proteomics, PTM mapping, intact mass and metabolite ID, processed in MaxQuant, DIA-NN and Compound Discoverer. Technique follows the question, and both classes of instrument sit in one laboratory.

When it comes to protein analysis, mass spectrometry offers an invaluable tool for determining molecular weight, sequence, modifications, and interactions. There are two main approaches for protein analysis: top-down and bottom-up. In top-down analysis, intact proteins are ionized and fragmented in the mass spectrometer, enabling the inference of protein structure and composition from the resulting spectra. In bottom-up analysis, proteins are digested into peptides using enzymes, such as trypsin. The peptides are then separated by liquid chromatography and analyzed by mass spectrometry. The resulting peptide sequences are matched to a protein database to identify the proteins and their modifications.

Peptide analysis, on the other hand, involves determining the molecular weight, sequence, composition, and modifications of peptides. Peptides can be ionized using electrospray or matrix-assisted laser desorption/ionization (MALDI) and analyzed by various types of mass analyzers, such as quadrupole, time-of-flight, ion trap, or orbitrap. Different fragmentation methods, such as collision-induced dissociation (CID), electron transfer dissociation (ETD), or higher-energy collisional dissociation (HCD), are employed to generate sequence-specific ions for peptide identification.

And let’s not forget about oligonucleotide analysis. Mass spectrometry is invaluable in determining the molecular weight, sequence, composition, and modifications of oligonucleotides. These short strands of nucleic acids, such as DNA or RNA, can be synthesized or extracted from biological sources. Oligonucleotides can be ionized using electrospray or MALDI and analyzed by various types of mass analyzers, such as quadrupole, time-of-flight, ion trap, or orbitrap. Oligonucleotide fragmentation can be induced by different methods, such as CID, ETD, or in-source decay (ISD), to generate sequence-specific ions that enable accurate identification of the oligonucleotide and its modifications.

Simply. You describe the question and the sample; a written scope and timeline come back within two business days. Samples ship with submission guidance we provide, the analysis runs, and results return with interpretation and the raw instrument files delivered alongside, so your own team can reprocess or audit later. If the question would be answered better on a different platform in this building, we say so before you spend.

Triple quadrupole answers how much: validated quantitation of a known analyte at the lowest defensible concentration. HRMS answers what is it: accurate mass to identify an unknown metabolite, place a modification, resolve isoforms, or characterize an intact protein. Many programs need both in sequence, identify on the Orbitrap, then quantify on the triple quad, and both live in this building, so the handoff is a corridor, not a contract.

Yes. Raw instrument files are delivered with the processed results, not archived out of reach, so your own informatics team can reprocess, audit or mine the data later. Discovery work that may face regulators someday deserves data that travels.

Yes, that is what SISCAPA-style immunocapture with LC-MRM is for: a single anti-peptide antibody enriches the target after digestion, isotope-labeled internal standards anchor the quantitation, and the mass spectrometer supplies the specificity an immunoassay would have begged from a second antibody. It is the standard route for novel targets and difficult matrices where ligand binding has no reagents to stand on.

Yes. Formalin-fixed paraffin-embedded tissue runs in the discovery and targeted proteomics workflows: extraction and digestion are adapted for crosslinked samples, and label-free DDA or DIA quantitation proceeds from there. FFPE archives hold biology no fresh cohort can replace, and rescuing that signal is a routine request here.